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At least 127 records · Page 7Linked to original sources

Mechanical properties of calcified exoskeleton from the neotropical millipede, Nyssodesmus python.

The calcified exoskeleton of millipedes plays a crucial role in resisting large forces developed during burrowing locomotion. I measured morphological and mechanical properties of cuticle from the neotropical forest floor millipede, Nyssodesmus python (Diplopoda: Polydesmidae), which ranges in body mass from 2 to 7 g. Scaling of thickness of the cuticle with respect to body mass followed predictions of geometric similarity. Both fracture strength and Young's modulus increased with body mass in females but not in males. In spite of their smaller size, male millipedes were still stronger, on average, than female millipedes. Mean fracture strength of millipede cuticle was 124 MPa, and Young's modulus was 17 GPa. Both of these values exceed measurements from typical insect cuticle, suggesting that calcium salts may play a role in stiffening and strengthening the millipede exoskeleton. Because of the high density of calcified millipede cuticle (1660 kg/m3), stiffness and strength relative to body weight remain comparable to values for other insect cuticles. These results corroborate a previous hypothesis that absolute not specific strength and stiffness have been selective factors in the evolution of millipede cuticle, and that bulkiness of the exoskeleton has been minimized through the deposition of calcium salts.

Animals↗

Phylogeographic analysis of the green python, Morelia viridis, reveals cryptic diversity.

Green pythons, which are regionally variable in colour patterns, are found throughout the lowland rainforest of New Guinea and adjacent far northeastern Australia. The species is popular in commercial trade and management of this trade and its impacts on natural populations could be assisted by molecular identification tools. We used mitochondrial nucleotide sequences and a limited allozyme data to test whether significantly differentiated populations occur within the species range. Phylogenetic analysis of mtDNA sequences revealed hierarchal phylogeographic structure both within New Guinea and between New Guinea and Australia. Strongly supported reciprocally monophyletic mitochondrial lineages, northern and southern, were found either side of the central mountain range that runs nearly the length of New Guinea. Limited allozyme data suggest that population differentiation is reflected in the nuclear as well as the mitochondrial genome. A previous morphological analysis did not find any phenotypic concordance with the pattern of differentiation observed in the molecular data. The southern mitochondrial lineage includes all of the Australian haplotypes, which form a single lineage, nested among the southern New Guinean haplotypes.

Alleles↗

Functional site of endogenous phospholipase A2 inhibitor from python serum.

The functional site of 'phospholipase A2 inhibitor from python' (PIP) was predicted based on the hypothesis of proline brackets. Using different sources of secretory phospholipase A2 (sPLA2s) as enzyme, and [3H]arachidonate-labelled Escherichia coli as substrate, short synthetic peptides representing the proposed site were examined for their secretory phospholipase A2 (sPLA2) inhibitory activity. A decapeptide P-PB.III proved to be the most potent of the tested peptides in inhibiting sPLA2 enzymatic activity in vitro, and exhibited striking anti-inflammatory effects in vivo in a mouse paw oedema model. P-PB.III inhibited the enzymatic activity of class I, II and III PLA2s, including that of human synovial fluid from arthritis patients. When tested by ELISA, biotinylated P-PB.III interacted positively with various PLA2s, suggesting that the specific region of PIP corresponding to P-PB.III, is likely to be involved in the PLA2-PLI interaction. The effect of P-PB.III on the peritoneal inflammatory response after surgical trauma in rats was also examined. P-PB.III effectively reduced the extent of postsurgical peritoneal adhesions as compared to controls. sPLA2 levels at seventh postoperative day in the peritoneal tissue of P-PB.III-treated rats were also significantly reduced (P < 0.05) in comparison to those of the untreated controls. The present results shed additional insight on the essential structural elements for PLA2 binding, and may be useful as a basis for the design of novel therapeutic agents.

Amino Acid Sequence↗

ScrumPy: metabolic modelling with Python.

ScrumPy is a software package used for the definition and analysis of metabolic models. It is written using the Python programming language that is also used as a user interface. ScrumPy has features for both kinetic and structural modelling, but the emphasis is on structural modelling and those features of most relevance to analysis of large (genome-scale) models. The aim is at describing ScrumPy's functionality to readers with some knowledge of metabolic modelling, but implementation, programming and other computational details are omitted. ScrumPy is released under the Gnu Public Licence, and available for download from http://mudshark.brookes.ac.uk/ ScrumPy.

Adaptation, Physiological↗

SpatialRNA: a Python package for easy application of Graph Neural Network models on single-molecule spatial transcriptomics dataset.

SUMMARY: Image-based spatial transcriptomics (iST) deliver gene expression measurements of RNA transcripts in tissue slices with single-molecule resolution and spatial context preserved. Modern Graph Neural Network (GNN) models are promising methods for capturing the complex molecular and cellular phenotypes in tissues at single-transcript and single-cell levels. A key application of GNNs is the detection of spatial domains or niches, that is, groups of molecules and/or cells that collaboratively work together to produce complex phenotypes. Due to the vast number of detected transcripts in (iST) dataset, applying GNNs on RNA molecule graphs is not trivial. We present a Python package, SpatialRNA, for easy (sub)graph generation from tissue samples and provide comprehensive tutorials for convenient and efficient application of Graph Neural Network models under the PyG framework. This highly scalable tool comprehensively segments tissue into spatial domains, aiding in biological interpretation of iST data and its underlying molecular microenvironments. AVAILABILITY AND IMPLEMENTATION: The SpatialRNA package is freely accessible from online repository https://github.com/ruqianl/spatialrna and can be installed via pip. Comprehensive tutorials, guidance on parameter selection, and complete workflows of case studies are available from the documentation website https://ruqianl.github.io/spatialrna_docs/, and uploaded on Zenodo with a DOI 10.5281/zenodo.17339575.

Neural Networks, Computer↗

PyEvoMotion: a Python tool for population-based time-course analysis of genome evolution.

SUMMARY: We present PyEvoMotion, an open-source Python tool for inferring molecular clock models with time-dependent Gaussian noise from high-throughput genomic datasets. PyEvoMotion features a command-line interface and a modular architecture, allowing seamless integration into larger bioinformatic pipelines. The tool supports customizable filtering, temporal discretization definition, and mutation classification, making it adaptable to diverse research needs. While traditional phylogenetic methods may encounter computational challenges with large datasets, PyEvoMotion can process thousands to millions of sequences to compute statistical parameters associated with a stochastic differential equation model, thereby weighting the genetic variation within the population. Using viral genomic data, we demonstrate its capability to infer evolutionary rates and detect non-Brownian evolutionary motions with subdiffusive behavior. PyEvoMotion shows potential to provide overlooked insights into genome evolution in different contexts. AVAILABILITY AND IMPLEMENTATION: The open source software is available on GitHub at https://github.com/luksgrin/PyEvoMotion and on SourceForge at https://sourceforge.net/projects/pyevomotion.

Software↗

PDB file parser and structure class implemented in Python.

UNLABELLED: The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. AVAILABILITY: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org

Computer Simulation↗

Sarment: Python modules for HMM analysis and partitioning of sequences.

Sarment is a package of Python modules for easy building and manipulation of sequence segmentations. It provides efficient implementation of usual algorithms for hidden Markov Model computation, as well as for maximal predictive partitioning. Owing to its very large variety of criteria for computing segmentations, Sarment can handle many kinds of models. Because of object-oriented programming, the results of the segmentation are very easy tomanipulate.

Algorithms↗

Paternal alleles enhance female reproductive success in tropical pythons.

The conventional view that female reproductive success is unlikely to benefit from multiple mating has come under strong challenge in recent years. In the present study, we demonstrate that the time wild-caught reproductive female water pythons (Liasis fuscus) spent in the laboratory prior to oviposition affected both hatching success and the number of male microsatellite alleles detected in the broods. A negative correlation between time in captivity and number of male alleles observed in the broods suggests that reduced hatching success was most likely not caused by environmental factors such as non-optimal temperatures, but rather by restricted mating opportunities. Maternal nutritional status and mean hatchling mass did not affect brood viability. However, our results revealed a positive correlation between number of male microsatellite alleles observed in the broods and hatching success, suggesting that increased paternal genetic variability enhanced female reproductive success. As microsatellite loci are unlikely to be direct targets of selection, we suggest that variability at these loci may cosegregate with other polymorphic genes directly linked to fitness.

Alleles↗

Atrioventricular valvular insufficiency and congestive heart failure in a carpet python.

Right atrioventricular valve insufficiency and bilateral congestive heart failure were identified in a carpet python (Morelia spilota variegata) with the aid of colour Doppler echocardiography, electrocardiography and radiography. The snake failed to respond to diuretic therapy and was euthanased. Based on this case, it appears that bilateral congestive failure is feasible in univentricular animals with lesions restricted to one side of the heart. Loop diuretic therapy may be inappropriate in non-crocodilian reptiles because reptiles lack a loop of Henle.

Animals↗

Integrating computation and visualization for biomolecular analysis: an example using python and AVS.

One of the challenges in biocomputing is to enable the efficient use of a wide variety of fast-evolving computational methods to simulate, analyze, and understand the complex properties and interactions of molecular systems. Our laboratory investigates several areas including molecular visualization, protein-ligand docking, protein-protein docking, molecular surfaces, and the derivation of phenomenological potentials. In this paper we present an approach based on the Python programming language to achieve a high level of integration between these different computational methods and our primary visualization system AVS. This approach removes many limitations of AVS while increasing dramatically the inter-operability of our computational tools. Several examples are shown to illustrate how this approach enables a high level of integration and inter-operability between different tools, while retaining modularity and avoiding the creation of a large monolithic package that is difficult to extend and maintain.

Capsid↗

Systemic arterial hemodynamics in the diamond python Morelia spilotes.

Studies of pulsatile systemic arterial hemodynamics were conducted in 10 diamond python snakes to test the hypothesis that body shape--through spatial dispersion of peripheral reflecting sites--is an important determinant of impedance patterns and of pulse wave contour. Findings support the hypothesis. Flow patterns in the aortic roots were similar to those in humans, sheep, dogs, rabbits, and guinea pigs, but in contrast to larger animals, little change in flow contour was seen in other arteries. Pressure wave contour was similar in all systemic arteries from which records were taken with no secondary diastolic wave under any circumstances. Impedance patterns at different sites showed none of the fluctuations that in other animals are attributable to discrete wave reflection. Discrete proximal wave reflection at the confluence of aortic arches was minimal. Data are explicable on the basis of widely distributed peripheral reflecting sites--a consequence of the snake's long and tapered body.

Animals↗

Pulse-wave propagation in the arterial system of the diamond python Morelia spilotes.

Pulse-wave velocity (PWV) and pulse-wave amplification (PWA) were measured over a proximal [51 +/- 3 (SE) cm] and distal segment (60 +/- 6 cm) of the common descending aorta of 10 anesthetized diamond python snakes (Morelia spilotes). For proximal and distal segments, PWV values were 551 +/- 66 and 921 +/- 116 cm/s and PWA were 0.91 +/- 0.05 and 0.91 +/- 0.06, respectively. PWV for proximal and distal segments were significantly different (P less than 0.02), but PWA were not. PWA for separate harmonics of heart frequency showed no significant increase above unity. Increase of PWV between distal and proximal aorta indicates a reduction in arterial distensibility, a phenomenon that in other species is associated with amplification of the pressure pulse; this was not observed in snakes. Using a simple elastic tube model 56 cm in length and 3 mm in diameter it was found that the amplification produced by the measured PWV changes is offset by attenuation due to viscous damping. Thus similarity of pulse-wave contour throughout the snake's aorta is attributable to the opposing effects of elastic nonuniformity and viscous damping.

Animals↗

CountASAP: a lightweight, easy to use python package for processing ASAPseq data.

BACKGROUND: Declining sequencing costs coupled with the increasing availability of easy-to-use kits for the isolation of DNA and RNA transcripts from single cells have driven a rapid proliferation of studies centered around genomic and transcriptomic data. Simultaneously, a wealth of new techniques have been developed that utilize single cell technologies to interrogate a broad range of cell-biological processes. One recently developed technique, transposase-accessible chromatin with sequencing (ATAC) with select antigen profiling by sequencing (ASAPseq), provides a combination of chromatin accessibility assessments with measurements of cell-surface marker expression levels. While software exists for the characterization of these datasets, there currently exists no tool explicitly designed to reformat ASAP surface marker FASTQ data into a count matrix which can then be used for these downstream analyses. RESULTS: To address this lack of a dedicated tool for ASAPseq data processing, we created CountASAP, an easy-to-use Python package purposefully designed to transform FASTQ files from ASAP experiments into count matrices compatible with commonly-used downstream bioinformatic analysis packages. CountASAP takes advantage of the independence of the relevant data structures to perform fully parallelized matches of each sequenced read to user-supplied input ASAP oligos and unique cell-identifier sequences. We directly compare the performance and user-friendliness of CountASAP to existing tools using similarly-structured data from a more common sequencing experiment: cellular indexing of transcriptomes and epitopes by sequencing (CITEseq). Further benchmarking against existing tools helps to identify proper defaults for CountASAP and assess the agreement of outputs from all tested software. A final test using a novel ASAPseq dataset provides evidence that CountASAP can generate biologically meaningful results that correlate well with paired chromatin accessibility data. CONCLUSIONS: CountASAP shows good agreement with existing, well-tested data processing tools in the analysis of similarly-structured benchmarking data. CountASAP runs efficiently on a standard laptop, has user-friendly documentation, a one-step installation, and represents the first and only tool designed specifically for the processing of ASAPseq data.

Software↗

Ventricular haemodynamics in Python molurus: separation of pulmonary and systemic pressures.

Vascular pressure separation by virtue of a two-chambered ventricle evolved independently in mammals and birds from a reptilian ancestor with a single ventricle, and allowed for high systemic perfusion pressure while protecting the lungs from oedema. Within non-crocodilian reptiles, ventricular pressure separation has only been observed in varanid lizards and has been regarded as a unique adaptation to an active predatory life style and high metabolic rate. The systemic and pulmonary sides of the ventricle in Python molurus are well separated by the muscular ridge, and a previous study using in situ perfusion of the heart revealed a remarkable flow separation and showed that the systemic side can sustain higher output pressures than the pulmonary side. Here we extend these observations by showing that systemic blood pressure P(sys) exceeded pulmonary pressure P(pul) almost seven times (75.7+/-4.2 versus 11.6+/-1.1 cm H(2)O). The large pressure difference between the systemic and pulmonary circulation persisted when P(sys) was altered by infusion of sodium nitroprusside or phenylephrine. Intraventricular pressures, measured in anaesthetised snakes, showed an overlap in the pressure profile between the pulmonary side of the ventricle (cavum pulmonale) and the pulmonary artery, while the higher pressure in the systemic side of the ventricle (cavum arteriosum) overlapped with the pressure in the right aortic arch. This verifies that the pressure differences originate within the ventricle, indicating that the large muscular ridge separates the ventricle during cardiac contraction.

Animals↗

A three-dimensional kinematic analysis of tongue flicking in Python molurus.

The forked snake tongue is a muscular organ without hard skeletal support. A functional interpretation of the variable arrangement of the intrinsic muscles along the tongue requires a quantitative analysis of the motion performance during tongue protrusion and flicking. Therefore, high-speed fluoroscopy and high-speed stereo photogrammetry were used to analyse the three-dimensional shape changes of the tongue in Python molurus bivittatus (Boidae). The posterior protruding part of the tongue elongated up to 130% while the flicking anterior portion elongated maximally 60%. The differences in tongue strains relate to the absence or presence, respectively, of longitudinal muscle fibres in the peripheral tongue. Maximum overall protrusion velocity (4.3 m s(-1)) occurred initially when the tongue tip left the mouth. Maximum tongue length of approximately 0.01 body length (20 mm) was reached during the first tongue flick. These observations are discussed within the scope of the biomechanical constraints of hydrostatic tongue protrusion: a negative forward pressure gradient, longitudinal tongue compliance and axial tongue stiffness. The three-dimensional deformation varied along the tongue with a mean curvature of 0.06 mm(-1) and a maximum value of 0.5 mm(-1). At the basis of the anterior forked portion of the tongue tips, extreme curvatures up to 2.0 mm(-1) were observed. These quantitative results support previously proposed inferences about a hydrostatic elongation mechanism and may serve to evaluate future dynamic models of tongue flicking.

Animals↗

Pulmonary mycobacteriosis caused by Mycobacterium haemophilum and M. marinum in a royal python.

An adult female royal python was referred with an 18-month history of chronic respiratory tract disease. Anemia and moderate leukocytosis with heterophilia and monocytosis were detected and interpreted as evidence of a chronic inflammatory condition. Evaluation of lateral and dorsoventral radiographic views revealed multiple soft-tissue opacities within the cranial lung fields. Endoscopic evaluation revealed that the normal reticulated pattern on the surface of the lung had been largely replaced by diffuse, granulomatous tissue. Histologic examination of biopsy specimens revealed classic pyogranulomas. Ziehl-Neelsen stains revealed numerous acid-fast bacilli consistent with Mycobacterium spp. Molecular methods including polymerase chain reaction restriction assays and DNA sequencing confirmed the identification of M. haemophilum and M. marinum. The snake was euthanatized. Mycobacteriosis is an uncommon and sporadic pyogranulomatous disease of reptiles. In most cases of reptile mycobacteriosis, treatment is not advised because of the chronic nature and often advanced stage of the disease, long-term and expensive nature of potential treatment regimens, and the risk of spread to other animals, including humans.

Animals↗

First identification of a ranavirus from green pythons (Chondropython viridis).

Ten juvenile green pythons (Chondropython viridis) died or were euthanized shortly after having been illegally imported into Australia from Indonesia in 1998. Histologic examination of two of the three snakes that died revealed moderately severe chronic ulceration of the nasal mucosa and focal or periacinar degeneration and necrosis of the liver. In addition there was severe necrotizing inflammation of the pharyngeal submucosa accompanied by numerous macrophages, heterophils, and edema. An iridovirus was isolated in culture from several tissues and characterized by immunohistochemistry, electron microscopy, enzyme-linked immunosorbent Assay, polyacrylamide gel electrophoresis, polymerase chain reaction and sequence analysis, restriction endonuclease digestion, and DNA hybridization. This is the first report of a systemic ranavirus infection in any species of snake and is a new member of the genus, Ranavirus.

Amino Acid Sequence↗